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MultiQC: Summarize analysis results for multiple tools and samples in a single report
Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
Bioinformatics (2016)
doi: 10.1093/bioinformatics/btw354
PMID: 27312411

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About MultiQC

This report was generated using MultiQC, version 1.25.2

You can see a YouTube video describing how to use MultiQC reports here: https://youtu.be/qPbIlO_KWN0

For more information about MultiQC, including other videos and extensive documentation, please visit http://multiqc.info

You can report bugs, suggest improvements and find the source code for MultiQC on GitHub: https://github.com/MultiQC/MultiQC

MultiQC is published in Bioinformatics:

MultiQC: Summarize analysis results for multiple tools and samples in a single report
Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
Bioinformatics (2016)
doi: 10.1093/bioinformatics/btw354
PMID: 27312411

MultiQC is developed by:

A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

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Report generated on 2024-12-13, 00:42 CET based on data in: /home/oscar/Desktop/BioinformaticProjects/UpDownRegulated/Project/data/html/Filtered_Alignment

General Statistics

Showing ⁰/₁₈ rows and ⁵/₈ columns.

Sample Name	Error rate	Non-primary	Reads mapped	% Mapped	% Proper pairs	% MapQ 0 reads	Total seqs	Mean insert
SRR6984609_trimmed_sorted_quality	0.25%	5.5M	22.3M	100.0%	0.0%	1.8%	22.3M	0.0bp
SRR6984610_trimmed_sorted_quality	0.21%	6.7M	24.6M	100.0%	0.0%	1.7%	24.6M	0.0bp
SRR6984611_trimmed_sorted_quality	0.18%	5.9M	25.6M	100.0%	0.0%	1.2%	25.6M	0.0bp
SRR6984612_trimmed_sorted_quality	0.12%	5.1M	24.4M	100.0%	0.0%	0.7%	24.4M	0.0bp
SRR6984613_trimmed_sorted_quality	0.21%	5.8M	23.9M	100.0%	0.0%	1.5%	23.9M	0.0bp
SRR6984614_trimmed_sorted_quality	0.11%	5.2M	25.9M	100.0%	0.0%	0.7%	25.9M	0.0bp
SRR6984615_trimmed_sorted_quality	0.24%	6.3M	25.1M	100.0%	0.0%	1.8%	25.1M	0.0bp
SRR6984616_trimmed_sorted_quality	0.15%	6.8M	33.3M	100.0%	0.0%	1.0%	33.3M	0.0bp
SRR6984617_trimmed_sorted_quality	0.14%	6.1M	27.9M	100.0%	0.0%	1.0%	27.9M	0.0bp
SRR6984618_trimmed_sorted_quality	0.13%	6.1M	23.0M	100.0%	0.0%	1.0%	23.0M	0.0bp
SRR6984619_trimmed_sorted_quality	0.16%	7.0M	23.4M	100.0%	0.0%	1.4%	23.4M	0.0bp
SRR6984620_trimmed_sorted_quality	0.14%	5.6M	23.3M	100.0%	0.0%	1.1%	23.3M	0.0bp
SRR6984621_trimmed_sorted_quality	0.32%	5.7M	21.9M	100.0%	0.0%	2.4%	21.9M	0.0bp
SRR6984622_trimmed_sorted_quality	0.19%	5.3M	26.8M	100.0%	0.0%	1.1%	26.8M	0.0bp
SRR6984623_trimmed_sorted_quality	0.25%	8.6M	32.2M	100.0%	0.0%	2.0%	32.2M	0.0bp
SRR6984624_trimmed_sorted_quality	0.17%	7.0M	29.8M	100.0%	0.0%	1.1%	29.8M	0.0bp
SRR6984625_trimmed_sorted_quality	0.18%	5.5M	22.9M	100.0%	0.0%	1.3%	22.9M	0.0bp
SRR6984626_trimmed_sorted_quality	0.12%	5.4M	23.9M	100.0%	0.0%	0.9%	23.9M	0.0bp

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order. Table ID: general_stats_table_table

Sort	Group	Column	Description	ID	Scale
\|\|	Samtools: stats	Error rate	Error rate: mismatches (NM) / bases mapped (CIGAR)	`samtools_stats-error_rate`
\|\|	Samtools: stats	Non-primary	Non-primary alignments (millions)	`samtools_stats-non_primary_alignments`	read_count
\|\|	Samtools: stats	Reads mapped	Reads mapped in the bam file (millions)	`samtools_stats-reads_mapped`	read_count
\|\|	Samtools: stats	% Mapped	% Mapped reads	`samtools_stats-reads_mapped_percent`
\|\|	Samtools: stats	% Proper pairs	% Properly paired reads	`samtools_stats-reads_properly_paired_percent`
\|\|	Samtools: stats	% MapQ 0 reads	% of reads that are ambiguously placed (MapQ=0)	`samtools_stats-reads_MQ0_percent`
\|\|	Samtools: stats	Total seqs	Total sequences in the bam file (millions)	`samtools_stats-raw_total_sequences`	read_count
\|\|	Samtools: stats	Mean insert	Average insert size	`samtools_stats-insert_size_average`

Samtools

Version:


                      
                        1.13

Toolkit for interacting with BAM/CRAM files.URL: http://www.htslib.orgDOI: 10.1093/bioinformatics/btp352

Percent mapped

Alignment metrics from samtools stats; mapped vs. unmapped reads vs. reads mapped with MQ0.

For a set of samples that have come from the same multiplexed library, similar numbers of reads for each sample are expected. Large differences in numbers might indicate issues during the library preparation process. Whilst large differences in read numbers may be controlled for in downstream processings (e.g. read count normalisation), you may wish to consider whether the read depths achieved have fallen below recommended levels depending on the applications.

Low alignment rates could indicate contamination of samples (e.g. adapter sequences), low sequencing quality or other artefacts. These can be further investigated in the sequence level QC (e.g. from FastQC).

Reads mapped with MQ0 often indicate that the reads are ambiguously mapped to multiple locations in the reference sequence. This can be due to repetitive regions in the genome, the presence of alternative contigs in the reference, or due to reads that are too short to be uniquely mapped. These reads are often filtered out in downstream analyses.

Created with MultiQC

Alignment stats

This module parses the output from samtools stats. All numbers in millions.

Created with MultiQC

Showing ⁰/₁₈ rows and ¹³/₁₃ columns.

Sample Name	Total sequences	Mapped & paired	Properly paired	Duplicated	QC Failed	Reads MQ0	Mapped bases (CIGAR)	Bases Trimmed	Duplicated bases	Diff chromosomes	Other orientation	Inward pairs	Outward pairs
SRR6984609_trimmed_sorted_quality	22.3M	0.0M	0.0M	0.0M	0.0M	0.4M	1377.1Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
SRR6984610_trimmed_sorted_quality	24.6M	0.0M	0.0M	0.0M	0.0M	0.4M	1518.9Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
SRR6984611_trimmed_sorted_quality	25.6M	0.0M	0.0M	0.0M	0.0M	0.3M	1583.7Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
SRR6984612_trimmed_sorted_quality	24.4M	0.0M	0.0M	0.0M	0.0M	0.2M	1509.9Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
SRR6984613_trimmed_sorted_quality	23.9M	0.0M	0.0M	0.0M	0.0M	0.4M	1475.7Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
SRR6984614_trimmed_sorted_quality	25.9M	0.0M	0.0M	0.0M	0.0M	0.2M	1599.1Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
SRR6984615_trimmed_sorted_quality	25.1M	0.0M	0.0M	0.0M	0.0M	0.5M	1551.1Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
SRR6984616_trimmed_sorted_quality	33.3M	0.0M	0.0M	0.0M	0.0M	0.3M	2059.5Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
SRR6984617_trimmed_sorted_quality	27.9M	0.0M	0.0M	0.0M	0.0M	0.3M	1724.1Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
SRR6984618_trimmed_sorted_quality	23.0M	0.0M	0.0M	0.0M	0.0M	0.2M	1419.4Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
SRR6984619_trimmed_sorted_quality	23.4M	0.0M	0.0M	0.0M	0.0M	0.3M	1441.3Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
SRR6984620_trimmed_sorted_quality	23.3M	0.0M	0.0M	0.0M	0.0M	0.3M	1434.7Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
SRR6984621_trimmed_sorted_quality	21.9M	0.0M	0.0M	0.0M	0.0M	0.5M	1348.2Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
SRR6984622_trimmed_sorted_quality	26.8M	0.0M	0.0M	0.0M	0.0M	0.3M	1655.3Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
SRR6984623_trimmed_sorted_quality	32.2M	0.0M	0.0M	0.0M	0.0M	0.6M	1989.5Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
SRR6984624_trimmed_sorted_quality	29.8M	0.0M	0.0M	0.0M	0.0M	0.3M	1838.3Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
SRR6984625_trimmed_sorted_quality	22.9M	0.0M	0.0M	0.0M	0.0M	0.3M	1410.0Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M
SRR6984626_trimmed_sorted_quality	23.9M	0.0M	0.0M	0.0M	0.0M	0.2M	1479.8Mb	0.0Mb	0.0Mb	0.0M	0.0M	0.0M	0.0M

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order. Table ID: samtools-stats-dp_table-1

Sort	Column	Description	ID	Scale
\|\|	Total sequences	Total sequences	`raw_total_sequences`	read_count
\|\|	Mapped & paired	Paired-end technology bit set + both mates mapped	`reads_mapped_and_paired`	read_count
\|\|	Properly paired	Proper-pair bit set	`reads_properly_paired`	read_count
\|\|	Duplicated	PCR or optical duplicate bit set	`reads_duplicated`	read_count
\|\|	QC Failed	QC Failed	`reads_QC_failed`	read_count
\|\|	Reads MQ0	Reads mapped and MQ=0	`reads_MQ0`	read_count
\|\|	Mapped bases (CIGAR)	Mapped bases (CIGAR)	`bases_mapped__cigar`	base_count
\|\|	Bases Trimmed	Bases Trimmed	`bases_trimmed`	base_count
\|\|	Duplicated bases	Duplicated bases	`bases_duplicated`	base_count
\|\|	Diff chromosomes	Pairs on different chromosomes	`pairs_on_different_chromosomes`	read_count
\|\|	Other orientation	Pairs with other orientation	`pairs_with_other_orientation`	read_count
\|\|	Inward pairs	Inward oriented pairs	`inward_oriented_pairs`	read_count
\|\|	Outward pairs	Outward oriented pairs	`outward_oriented_pairs`	read_count

Software Versions

Software Versions lists versions of software tools extracted from file contents.

Software	Version
Samtools	`1.13`

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